Decoding Biomechanical Cues Based on DNA Sensors.

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Indentation Depth-Dependent Hardness of Metal-Organic Framework Crystals: The Effect of Local Amorphization Induced by Indentation.

The hardness of metal-organic frameworks (MOFs) is an important mechanical property metric measuring their resistance to the permanent plastic deformation. The hardness of most MOFs measured from nanoindentation experiments usually exhibits the similar unique indentation depth dependence feature, the mechanism of which still remains unclear. In order to explain the effect of the indentation depth on the hardness of MOFs, we conducted nanoindentation simulations on HKUST-1 by using reactive molecular dynamics simulations. Our simulations reveal that the HKUST-1 material near the indenter can transform from the parent crystalline phase to a new amorphous phase due to the high pressure generated, while its counterpart far from the indenter remains in the crystalline phase. By considering the crystalline-amorphous interface in the energy analysis of MOFs, we derived an analytical expression of the hardness at different indentation depths. It is found that the interface effect can greatly increase the hardness of MOFs, as observed in nanoindentation simulations. Moreover, the proposed analytical expression can well explain the indentation depth-dependent hardness of many MOF crystals measured in nanoindentation experiments. Overall, this work can provide a better understanding of the indentation depth dependence of the hardness of MOFs.

A new bacterial tRNA enhances antibiotic production in Streptomyces by circumventing inefficient wobble base-pairing.

We report the discovery and functional characterization of a new bacterial tRNA species. The tRNA-Asp-AUC, from a fast-growing desert streptomycete, decodes GAU codons. In the absence of queuosine tRNA anticodon modification in streptomycetes, the new tRNA circumvents inefficient wobble base-pairing during translation. The tRNA, which is constitutively expressed, greatly enhances synthesis of 4 different antibiotics in the model mesophilic species Streptomyces coelicolor, including the product of a so-called cryptic pathway, and increases yields of medically-important antibiotics in other species. This can be rationalised due to increased expression of both pleiotropic and pathway-specific transcriptional activators of antibiotic biosynthesis whose genes generally possess one or more GAT codons; the frequency of this codon in these gene sets is significantly higher than the average for streptomycete genes. In addition, the tRNA enhances production of cobalamin, a precursor of S-adenosyl methionine, itself an essential cofactor for synthesis of many antibiotics. The results establish a new paradigm of inefficient wobble base-pairing involving GAU codons as an evolved strategy to regulate gene expression and, in particular, antibiotic biosynthesis. Circumventing this by expression of the new cognate tRNA offers a generic strategy to increase antibiotic yields and to expand the repertoire of much-needed new bioactive metabolites produced by these valuable bacteria.

Nonribosomal antibacterial peptides isolated from Streptomyces agglomeratus 5-1-3 in the Qinghai-Tibet Plateau.

BACKGROUND: New antibiotics are urgently needed in clinical treatment of superdrug-resistant bacteria. Nonribosomal peptides (NRPs) are a major source of antibiotics because they exhibit structural diversity, and unique antibacterial mechanisms and resistance. Analysis of gene clusters of S. agglomeratus 5-1-3 showed that Clusters 3, 6, 12, 21, and 28 were used to synthesize NRPs. Here, we examined secondary metabolites of S. agglomeratus 5-1-3 isolated from soils in the Qinghai-Tibet Plateau, China, for NRPs with antibacterial activity. RESULTS: We isolated a total of 36 Streptomyces strains with distinct colony morphological characteristics from 7 soil samples. We screened 8 Streptomyces strains resistant to methicillin-resistant Staphylococcus aureus (MRSA). We then selected S. agglomeratus 5-1-3 for further study based on results of an antibacterial activity test. Here, we isolated three compounds from S. agglomeratus 5-1-3 and characterized their properties. The crude extract was extracted with ethyl acetate and purified with column chromatography and semipreparative high-performance liquid chromatography (HPLC). We characterized the three compounds using NMR analyses as echinomycin (1), 5,7,4'-trihydroxy-3.3',5'-trimethoxy flavone (2), and 2,6,2', 6'-tetramethoxy-4,4-bis(2,3-epoxy-1-hydroxypropyl)-biphenyl (3). We tested the antibacterial activity of pure compounds from strain 5-1-3 with the Oxford cup method. NRP echinomycin (1) showed excellent anti-MRSA activity with a minimum inhibitory concentration (MIC) of 2.0 µg/mL. Meanwhile, MIC of compound 2 and 3 was 128.0 µg/mL for both. In addition, 203 mg of echinomycin was isolated from 10 L of the crude extract broth of strain 5-1-3. CONCLUSION: In this study, S. agglomeratus 5-1-3 with strong resistance to MRSA was isolated from the soils in the Qinghai-Tibet Plateau. Strain 5-1-3 had a high yield of echinomycin (1) an NRP with a MIC of 2 µg/mL against MRSA. We propose that echinomycin derived from S. agglomeratus 5-1-3 may be a potent antibacterial agent for pharmaceutical use.

Comparative genomics reveals environmental adaptability and antimicrobial activity of a novel Streptomyces isolated from soil under black Gobi rocks.

A novel Streptomyces strain, designated 3_2T, was isolated from soil under the black Gobi rock sample of Northwest China. The taxonomic position of this strain was revealed by a polyphasic approach. Comparative analysis of the 16S rRNA gene sequences indicated that 3_2T was closely related to the members of the genus Streptomyces, with the highest similarity to Streptomyces rimosus subsp. rimosus CGMCC 4.1438 (99.17%), Streptomyces sioyaensis DSM 40032 (98.97%). Strain 3_2T can grow in media up to 13% NaCl. The genomic DNA G + C content of strain 3_2T was 69.9%. We obtained the genomes of 22 Streptomyces strains similar to strain 3_2T, compared the average nucleotide similarity, dDDH and average amino acid identity, and found that the genomic similarity of the new isolate 3_2T to all strains was below the threshold for interspecies classification. Chemotaxonomic data revealed that strain 3_2T possessed MK-9 (H6) and MK-9 (H8) as the major menaquinones. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugars were ribose and glucose. The major fatty acid methyl esters were iso-C16:0 (23.6%) and anteiso-C15:0 (10.4%). The fermentation products of strain 3_2T were inhibitory to Staphylococcus aureus and Bacillus thuringiensi. The genome of 3_2T was further predicted using anti-smash and the strain was found to encode the production of 41 secondary metabolites, and these gene clusters may be key to the good inhibitory activity exhibited by the strain. Genomic analysis revealed that strain 3_2T can encode genes that produce a variety of genes in response to environmental stresses, including cold shock, detoxification, heat shock, osmotic stress, oxidative stress, and these genes may play a key role in the harsh environment in which the strain can survive. Therefore, this strain represents a novel Streptomyces species, for which the name Streptomyces halobius sp. nov. is proposed. The type strain is 3_2T (= JCM 34935T = GDMCC 4.217T).

BIRC5 Inhibition Is Associated with Pyroptotic Cell Death via Caspase3-GSDME Pathway in Lung Adenocarcinoma Cells.

Lung adenocarcinoma (LUAD) is a prevalent type of thoracic cancer with a poor prognosis and high mortality rate. However, the exact pathogenesis of this cancer is still not fully understood. One potential factor that can contribute to the development of lung adenocarcinoma is DNA methylation, which can cause changes in chromosome structure and potentially lead to the formation of tumors. The baculoviral IAP repeat containing the 5 (BIRC5) gene encodes the Survivin protein, which is a multifunctional gene involved in cell proliferation, migration, and invasion of tumor cells. This gene is elevated in various solid tumors, but its specific role and mechanism in lung adenocarcinoma are not well-known. To identify the potential biomarkers associated with lung adenocarcinoma, we screened the methylation-regulated differentially expressed genes (MeDEGs) of LUAD via bioinformatics analysis. Gene ontology (GO) process and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to investigate the biological function and pathway of MeDEGs. A protein-protein interaction (PPI) network was employed to explore the key module and screen hub genes. We screened out eight hub genes whose products are aberrantly expressed, and whose DNA methylation modification level is significantly changed in lung adenocarcinoma. BIRC5 is a bona fide marker which was remarkably up-regulated in tumor tissues. Flow cytometry analysis, lactate dehydrogenase release (LDH) assay and Micro-PET imaging were performed in A549 cells and a mouse xenograft tumor to explore the function of BIRC5 in cell death of lung adenocarcinoma. We found that BIRC5 was up-regulated and related to a high mortality rate in lung adenocarcinoma patients. Mechanically, the knockdown of BIRC5 inhibited the proliferation of A549 cells and induced pyroptosis via caspase3/GSDME signaling. Our findings have unraveled that BIRC5 holds promise as a novel biomarker and therapeutic target for lung adenocarcinoma. Additionally, we have discovered a novel pathway in which BIRC5 inhibition can induce pyroptosis through the caspase3-GSDME pathway in lung adenocarcinoma cells.

Conserving Semantic Unit Information and Simplifying Syntactic Constituents to Improve Implicit Discourse Relation Recognition.

Implicit discourse relation recognition (IDRR) has long been considered a challenging problem in shallow discourse parsing. The absence of connectives makes such relations implicit and requires much more effort to understand the semantics of the text. Thus, it is important to preserve the semantic completeness before any attempt to predict the discourse relation. However, word level embedding, widely used in existing works, may lead to a loss of semantics by splitting some phrases that should be treated as complete semantic units. In this article, we proposed three methods to segment a sentence into complete semantic units: a corpus-based method to serve as the baseline, a constituent parsing tree-based method, and a dependency parsing tree-based method to provide a more flexible and automatic way to divide the sentence. The segmented sentence will then be embedded at the level of semantic units so the embeddings could be fed into the IDRR networks and play the same role as word embeddings. We implemented our methods into one of the recent IDRR models to compare the performance with the original version using word level embeddings. Results show that proper embedding level better conserves the semantic information in the sentence and helps to enhance the performance of IDRR models.

Efficient degradation of hydroquinone by a metabolically engineered Pseudarthrobacter sulfonivorans strain.

Pseudarthrobacter sulfonivorans strain Ar51 can degrade crude oil and multi-substituted benzene compounds efficiently at low temperatures. However, it cannot degrade hydroquinone, which is a key intermediate in the degradation of several other compounds of environmental importance, such as 4-nitrophenol, g-hexachlorocyclohexane, 4-hydroxyacetophenone and 4-aminophenol. Here we co-expressed the two subunits of hydroquinone dioxygenase from Sphingomonas sp. strain TTNP3 with different promoters in the strain Ar51. The strain with 2 hdnO promoters exhibited the strongest hydroquinone catabolic activity. However, in the absence of antibiotic selection this ability to degrade hydroquinone was lost due to plasmid instability. Consequently, we constructed a hisD knockout strain, which was unable to synthesise histidine. By introducing the hisD gene onto the plasmid, the ability to degrade hydroquinone in the absence of antibiotic selection was stabilised. In addition, to make the strain more stable for industrial applications, we knocked out the recA gene and integrated the hydroquinone dioxygenase genes at this chromosomal locus. This strain exhibited the strongest activity in catabolizing hydroquinone, up to 470 mg/L in 16 h without antibiotic selection. In addition, this activity was shown to be stable when the strain has cultured in medium without antibiotic selection after 20 passages.

Risk Factors and Pathogen Spectrum in Continuous Ambulatory Peritoneal Dialysis-Associated Peritonitis: A Single Center Retrospective Study.

BACKGROUND To investigate the incidence, risk factors, pathogen distribution, and drug resistance patterns in continuous ambulatory peritoneal dialysis-associated peritonitis (CAPDP). MATERIAL AND METHODS Clinical data for 248 patients who underwent continuous ambulatory peritoneal dialysis (CAPD) treatment in a single center in China from March 2018 to January 2021 were retrospectively collected. The patients were divided into the CAPDP group (n=40) and the non-CAPDP group (n=208) according to whether peritonitis occurred. The incidence rate, risk factors, bacterial distribution, and drug sensitivity of CAPDP were analyzed. RESULTS The incidence of CAPDP was 16.13%, and 87.5% of patients with CAPDP continued CAPDP treatment after anti-infection treatment. Patients with and without CAPDP were clearly distinguished, on the basis of their clinical characteristics, by using principal component analysis (PCA) methods. Logistic regression analysis found that body mass index (BMI; P=0.0095), albumin (P=0.016), albumin/globulin ratio (P=0.018), C-reactive protein (P=0.0001), and rapid transport (P=0.034) were independent risk factors for CAPDP. The main pathogens causing the CAPDP were Staphylococcus epidermidis (50.00%), Staphylococcus capitis (13.33%), and Escherichia coli (10.00%). Among the pathogenic bacteria, the main drugs to which gram-negative cocci were sensitive were imipenem, meropenem, piperacillin/tazobactam, cefoperazone/sulbactam, ceftazidime, and tigecycline. The main drugs to which gram-positive cocci were sensitive were vancomycin, teicoplanin, and linezolid. The drug resistance rate of pathogenic bacteria to penicillin G, ampicillin, compound trimethoprim, cefepime, ceftriaxone, and amoxicillin-clavulanic acid drugs was 36.26-100%. CONCLUSIONS BMI, albumin, albumin/globulin ratio, C-reactive protein, and rapid transport are independent risk factors for CAPDP. Gram-positive bacteria are the main pathogens of CAPDP and are sensitive to vancomycin, teicoplanin, and linezolid.

Knockdown of lncRNA TTTY15 alleviates myocardial ischemia-reperfusion injury through the miR-374a-5p/FOXO1 axis.

Myocardial ischemia/reperfusion (I/R) injury greatly contributes to myocardial tissue damage in patients with coronary disease, which eventually leads to heart failure. Long noncoding RNAs (lncRNAs) have an emerging role in the process of myocardial I/R injury. Our previous work revealed the protective role of miR-374a-5p against myocardial I/R injury. In this study, we explored the role of lncRNA TTTY15 and its potential interaction mechanisms with miR-374a-5p in myocardial I/R injury. The expression of TTTY15 was increased both in vitro and in vivo after myocardial I/R injury models according to quantitative real-time polymerase chain reaction. Various assays were conducted to evaluate the regulatory relationship among TTTY15, miR-374a-5p, FOXO1, and autophagy in H9c2 and HL-1 cells. The results showed that TTTY15 suppresses autophagy and myocardial I/R injury by targeting miR-374a-5p. We found that TTTY15 regulates miR-374a-5p, thus affecting FOXO1 expression and autophagy in myocytes during I/R. Furthermore, in an in vivo mouse model of myocardial I/R injury, suppression of TTTY15 successfully alleviated myocardial I/R injury. Our results reveal a novel feedback mechanism in which TTTY15 regulates miRNA processing and a potential target in myocardial I/R injury. TTTY15 is a promising therapeutic target for treating myocardial I/R injury.

Circ-Zfp644 acts as a pro-hypertrophic mediator in an Ang-II induced in vitro myocardial hypertrophy model.

Cardiac hypertrophy (CH) is a common risk factor for heart failure and even sudden cardiac death. Molecules have emerged as vital regulators in cardiac disorders. LIM domain kinase 1 (Limk1) is reported as a pro-fibrotic mediator in patients with permanent atrial fibrillation and it has also been suggested to aggravate cardiac dysfunction in rats with chronic heart failure. The present study observed that Limk1 was significantly upregulated in the in vitro model of CH induced by angiotensin II (Ang-II). Interestingly, silencing Limk1 led to inhibition of the hypertrophic phenotypes in Ang-II-treated cardiomyocytes. Next, through a series of mechanistic assays including RIP assay, RNA pull-down assay, and luciferase reporter assay, miR-93-5p was verified to target Limk1. Furthermore, circ-Zfp644 was validated as the sponge of miR-93-5p. Circ-Zfp644 functioned as a ceRNA to upregulate Limk1 expression via sequestering miR-93-5p in Ang-II-treated cardiomyocytes. Finally, a range of rescue assays revealed that circ-Zfp644 stimulated hypertrophic effects in Ang-II-treated cardiomyocytes via upregulating Limk1 while miR-93-5p exerted the opposite effects via its inhibition on Limk1. On the whole, the present study revealed that circ-Zfp644 aggravated CH through modulating the miR-93-5p/Limk1 axis. The findings observed on the in vitro model of CH provided new potential for developing CH treatment.

An antifouling polymer for dynamic anti-protein adhesion analysis by a quartz crystal microbalance.

Nowadays, the non-specific adsorption of biomolecules is a key issue in numerous fields. Herein, an improved antifouling molecule was synthesized by grafting phenol with oligopoly (ethylene glycol), named (4-(2-(2-ethoxyethoxy) ethoxy) phenol (EEP). An ideal antifouling polymer coating (PEEP) was synthesized by the mechanism of electropolymerization of phenol. Quartz crystal microbalance (QCM), a sensitive mass sensor, was used to dynamically monitor both the modification and anti-protein adhesion (with bovine serum albumin as the model) process. Quantitatively, less proteins were observed to adhere to the modified electrode (277.8 ng for bare GCE and 8.88 ng for the modified GCE). Fourier transform infrared spectrophotometry (FT-IR), scanning electron microscopy (SEM), and electrochemical methods were used to study the coatings in detail. In this study, EEP was synthesized for the electrochemical preparation of an antifouling coating and characterized by QCM and electrochemical methods. The mild preparation environment (lower potential window and in phosphate buffered saline) and one-step method enable potential applications of PEEP in the field of biomaterials and biosensors.

A trehalose biosynthetic enzyme doubles as an osmotic stress sensor to regulate bacterial morphogenesis.

The dissacharide trehalose is an important intracellular osmoprotectant and the OtsA/B pathway is the principal pathway for trehalose biosynthesis in a wide range of bacterial species. Scaffolding proteins and other cytoskeletal elements play an essential role in morphogenetic processes in bacteria. Here we describe how OtsA, in addition to its role in trehalose biosynthesis, functions as an osmotic stress sensor to regulate cell morphology in Arthrobacter strain A3. In response to osmotic stress, this and other Arthrobacter species undergo a transition from bacillary to myceloid growth. An otsA null mutant exhibits constitutive myceloid growth. Osmotic stress leads to a depletion of trehalose-6-phosphate, the product of the OtsA enzyme, and experimental depletion of this metabolite also leads to constitutive myceloid growth independent of OtsA function. In vitro analyses indicate that OtsA can self-assemble into protein networks, promoted by trehalose-6-phosphate, a property that is not shared by the equivalent enzyme from E. coli, despite the latter's enzymatic activity when expressed in Arthrobacter. This, and the localization of the protein in non-stressed cells at the mid-cell and poles, indicates that OtsA from Arthrobacter likely functions as a cytoskeletal element regulating cell morphology. Recruiting a biosynthetic enzyme for this morphogenetic function represents an intriguing adaptation in bacteria that can survive in extreme environments.

Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation.

A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3 Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.

Streptomyces dangxiongensis sp. nov., isolated from soil of Qinghai-Tibet Plateau.

A novel actinobacterial strain, designated Z022T, isolated from a soil sample collected from Dangxiong in Tibet Autonomous Region (PR China), was determined by polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces. Strain Z022T showed high similarity value to Streptomyces lucensis NBRC 13056T (98.87 %) and S. achromogenes subsp. achromogenes NBRC 12735T (98.68 %) based on the 16S rRNA gene phylogenetic tree. The genomic DNA G+C content of strain Z022T based on the genome sequence was 72.16 mol%. DNA-DNA relatedness values between strain Z022T and strain Streptomyces lucensis NBRC 13056T was 23.7±1.3 % and significantly lower than 70 %. Chemotaxonomic data revealed that strain Z022T possessed MK-9(H8) and MK-9(H6) as the predominant menaquinone, ll-diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose, xylose and ribose as whole cell sugars. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the predominant polar lipids; anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z022T (=JCM 31053T=CGMCC 4.7273T) should be classified in the genus Streptomyces as Streptomyces dangxiongensis sp. nov.

The Mitochondrial tRNAAla T5655C Mutation May Modulate the Phenotypic Expression of tRNAMet and tRNAGln A4401G Mutation in a Han Chinese Family With Essential Hypertension.

Mutations in mitochondrial DNA are associated with the pathogenesis of essential hypertension. We report here the clinical, genetic, and molecular characterization of a three-generation Han Chinese family with essential hypertension. Most strikingly, this family exhibited a high penetrance of essential hypertension. Sequence analysis of the mitochondrial genome showed the presence of a homoplasmic T5655C mutation in tRNAAla, together with the A4401G mutation in the adjacent region between tRNAMet and tRNAGln. Notably, the T5655C mutation was localized at the acceptor arm of tRNAAla, disrupted the high conserved base-pairing (1A-72T), and may impair the tRNA function. Moreover, the A4401G mutation was reported to decrease the steady-state level of tRNAMet and tRNAGln, and consequently caused the mitochondrial dysfunction responsible for hypertension. Taken together, the combination of T5655C and A4401G mutations in mitochondrial tRNA genes may account for the high penetrance and expressivity of hypertension in this Chinese family. Thus, our findings may provide new insight into the pathogenesis of this disorder.

Streptomyces lacrimifluminis sp. nov., a novel actinobacterium that produces antibacterial compounds, isolated from soil.

A novel actinobacterial strain, designated Z1027T, was isolated from a soil sample collected near the Tuotuo River, Qinghai-Tibet Plateau (China). The strain exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus. The taxonomic position of strain Z1027T was determined using a polyphasic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree, together with Streptomyces turgidiscabies ATCC 700248T (99.19 % similarity), Streptomyces graminilatus JL-6T (98.84 %) and Streptomyces reticuliscabiei CFBP 4531T (98.36 %). The genomic DNA G+C content of strain Z1027T was 74±1 mol%. The DNA-DNA relatedness values between strain Z1027T and Streptomyces turgidiscabies ATCC 700248T and Streptomyces reticuliscabiei CFBP 4531T were 38.5±0.4 and 26.2±1.2 %, respectively, both of them significantly lower than 70 %. Chemotaxonomic data revealed that strain Z1027T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, ll-diaminopimelic acid as the diagnostic diamino acid and galactose as a whole-cell sugar. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatydilinositol and seven other unknown polar lipids were detected; iso-C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1027T (=CGMCC 4.7272T=JCM 31054T) should be classified as the type strain of a novel species of the genus Streptomyces,Streptomyces lacrimifluminis sp. nov.

Evolution of threonine aldolases, a diverse family involved in the second pathway of glycine biosynthesis.

Threonine aldolases (TAs) catalyze the interconversion of threonine and glycine plus acetaldehyde in a pyridoxal phosphate-dependent manner. This class of enzymes complements the primary glycine biosynthetic pathway catalyzed by serine hydroxymethyltransferase (SHMT), and was shown to be necessary for yeast glycine auxotrophy. Because the reverse reaction of TA involves carbon-carbon bond formation, resulting in a ß-hydroxyl-α-amino acid with two adjacent chiral centers, TAs are of high interests in synthetic chemistry and bioengineering studies. Here, we report systematic phylogenetic analysis of TAs. Our results demonstrated that L-TAs and D-TAs that are specific for L- and D-threonine, respectively, are two phylogenetically unique families, and both enzymes are different from their closely related enzymes SHMTs and bacterial alanine racemases (ARs). Interestingly, L-TAs can be further grouped into two evolutionarily distinct families, which share low sequence similarity with each other but likely possess the same structural fold, suggesting a convergent evolution of these enzymes. The first L-TA family contains enzymes of both prokaryotic and eukaryotic origins, and is related to fungal ARs, whereas the second contains only prokaryotic L-TAs. Furthermore, we show that horizontal gene transfer may occur frequently during the evolution of both L-TA families. Our results indicate the complex, dynamic, and convergent evolution process of TAs and suggest an updated classification scheme for L-TAs.

LC3B, a Protein That Serves as an Autophagic Marker, Modulates Angiotensin II-induced Myocardial Hypertrophy.

LC3B is a marker of autophagic activity, and growing evidence supports its importance in myocardial hypertrophy. Thus, regulating LC3B expression may provide an important avenue to inhibit autophagy and protect against or inhibit pathological myocardial hypertrophy. To address this question, we investigated the effects of altering LC3B mRNA expression and autophagic activity in the setting of cardiomyocyte hypertrophy. In an in vitro angiotensin II (Ang II)-induced cardiomyocyte hypertrophy model, LC3B mRNA and protein expression was increased and there was activation of cardiomyocyte autophagy, which was assessed by transmission electron microscopy and flow cytometry. LC3B cDNA transfection also resulted in an upregulation of autophagic activity, whereas downregulation of autophagic activity was observed with knockdown of LC3B expression. Induction of LC3B expression was shown to further exacerbate Ang II-stimulated cardiomyocyte hypertrophy, whereas inhibition of LC3B expression inhibited the Ang II-stimulated cardiomyocyte hypertrophy (as assessed through cardiomyocyte morphology and expression of ANP and ß-MHC). This study demonstrated that LC3B modulates the Ang II-induced cardiomyocyte hypertrophy in cultured neonatal rat ventricular cardiomyocytes.

Identification of potential pathogenic hepatic super-enhancers regulatory network in high-fat diet induced hyperlipidemia.

Hyperlipidemia (HLP) is a prevalent metabolic disorder and a significant risk factor for cardiovascular disease. According to recent discoveries, super-enhancers (SEs) play a role in the increased expression of genes that encode important regulators of both cellular identity and the progression of diseases. However, the underlying function of SEs in the development of HLP is still unknown. We performed an integrative analysis of data on H3K27ac ChIP-seq and RNA sequencing obtained from liver tissues of mice under a low-fat diet (LFD) and high-fat diet (HFD) from GEO database. The rank ordering of super enhancers algorithm was employed for the computation and identification of SEs. A total of 1,877 and 1,847 SEs were identified in the LFD and HFD groups, respectively. The SE inhibitor JQ1 was able to potently reverse lipid deposition and the increased intracellular triglyceride and total cholesterol induced by oleic acid, indicating that SEs are involved in regulating lipid accumulation. Two hundred seventy-eight were considered as HFD-specific SEs (HSEs). GO and KEGG pathway enrichment analysis of the upregulated HSEs-associated genes revealed that they were mainly involved in lipid metabolic pathway. Four hub genes, namely Cd36, Pex11a, Ech1, and Cidec, were identified in the HSEs-associated protein-protein interaction network, and validated with two other datasets. Finally, we constructed a HSEs-specific regulatory network with Cidec and Cd36 as the core through the prediction and verification of transcription factors. Our study constructed a HSEs-associated regulatory network in the pathogenesis of HLP, providing new ideas for the underlying mechanisms and therapeutic targets of HLP.